[Bioperl-l] How to read seq and quals into Bio::Seq::Quality object?

Florent Angly florent.angly at gmail.com
Mon Jun 30 15:34:00 EDT 2008


I have looked at the issue before and haven't found an existing way that 
import nicely a FASTA and QUAL file at the same time. It would be 
valuable in my opinion, but at the moment I think you have to create two 
SeqIO objects and go through all the sequence records in both of them 
simultaneously.
Florent


Phillip San Miguel wrote:
>    Anyone? Sorry if I'm being a jerk. But on the basis of the 
> existence of Bio::Seq::Quality it seems Bio::Seq::SeqWithQuality was 
> deprecated. But the latter has a clear methodology to get from .fasta 
> and .fasta.qual files into a new object. Once the new object is 
> populated, looks like the former might be superior to use.
>    But at the moment the only way I'm seeing to populate the ::Quality 
> object from two files is to bring each file in with SeqIO and then use 
> the primary seq and primary qual objects.  Thus created I'd export 
> their sequence and quals as text and use that create the ::Quality 
> object. If that is the way to go, fine. But I feel like I must be 
> missing something.
>
> Phillip
> Purdue Genomics Core Facility
>
> Phillip SanMiguel wrote:
>> What would be the accepted method to read the seq and qual values in 
>> from two files (a fasta and a qual file) and put them into 
>> Bio::Seq::Quality object. Is there a Bio::SeqIO method that would do 
>> that?
>>
>> Phillip
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